l" , "hcp-users@humanconnectome.org"
, Ido Tavor , Niv Tik
Subject: Re: [HCP-Users] HCP_FIX
You can specify your own training for to hcp_fix as an optional last argument.
Matt.
From: Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Thursday, December 13, 2018 at 6:39 AM
To: Ma
stl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>, Ido
Tavor mailto:idota...@gmail.com>>, Niv Tik
mailto:niv...@gmail.com>>
Subject: Re: [HCP-Users] HCP_FIX
if I understand correctly, what happens i
gt; hcp-users@humanconnectome.org>, Ido Tavor , Niv Tik <
> niv...@gmail.com>
> Subject: Re: [HCP-Users] HCP_FIX
>
> I'm sorry if I'm pressing the issue too much, but I still can't see how
> the hcp_fix solves the fact the the main FIX script expects several files
&
anconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>, Ido
Tavor mailto:idota...@gmail.com>>, Niv Tik
mailto:niv...@gmail.com>>
Subject: Re: [HCP-Users] HCP_FIX
I'm sorry if I'm pressing the issue too much, but I still can't
2018 at 7:47 AM
> To: "Harms, Michael"
> Cc: Matt Glasser , "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>, Ido Tavor
> Subject: Re: [HCP-Users] HCP_FIX
>
> hey again,
>
> thanks for pointing out the relevant lines for the dual regr
December 11, 2018 at 5:21 AM
> To: Matt Glasser
> Cc: "Harms, Michael" , "hcp-users@humanconnectome.org" <
> hcp-users@humanconnectome.org>, Ido Tavor
> Subject: Re: [HCP-Users] HCP_FIX
>
> hey Matt,
> I was trying to use the FIX s
AM
To: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "Harms, Michael" mailto:mha...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>, Ido
Tavor mailto:idota...@gmail.com>>
Sub
stl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>, Ido
Tavor mailto:idota...@gmail.com>>
Subject: Re: [HCP-Users] HCP_FIX
hey again,
thanks for pointing out the relevant lines for the dual regression.
I h
ve.Tel: 314-747-6173
>
> St. Louis, MO 63110 Email: mha...@wustl.edu
>
>
>
> *From: * on behalf of Shachar Gal <
> gal.shac...@gmail.com>
> *Date: *Friday, November 23, 2018 at 2:37 AM
> *To: *"Glasser, Matthew&
tthew"
Cc: "hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users] HCP_FIX
hey matt,
the thing is, I didn't see anything in the hip_fix script the projects the "fix
cleaned" volume to surface, so when does that happen?
considering that you mentioned you're
behalf of "Glasser,
> Matthew"
> *Date: *Thursday, November 22, 2018 at 8:29 AM
> *To: *Shachar Gal
> *Cc: *"hcp-users@humanconnectome.org"
> *Subject: *Re: [HCP-Users] HCP_FIX
>
>
>
> hcp_fix cleans both the volume and CIFTI data in parallel. If you r
;>
>> 660 South Euclid Ave.Tel: 314-747-6173
>>
>> St. Louis, MO 63110 Email: mha...@wustl.edu
>>
>>
>>
>> *From: * on behalf of "Glasser,
>> Matthew"
>> *Date: *Thursday, November 22
ed and tested
> and we will have new versions announced soon. PostFix generates the
> Workbench scenes for hand classification of components.
>
> Matt.
>
> From: on behalf of Shachar Gal <
> gal.shac...@gmail.com>
> Date: Monday, November 19, 2018 at 3:30 AM
> To: &qu
rs@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>, Ido
Tavor mailto:idota...@gmail.com>>
Subject: Re: [HCP-Users] HCP_FIX
and if I can be more specific on what we don't really understand regarding the
procedure-
the procedure when using FSL's FIX is
-6173
St. Louis, MO 63110 Email: mha...@wustl.edu
From: on behalf of "Glasser, Matthew"
Date: Thursday, November 22, 2018 at 8:29 AM
To: Shachar Gal
Cc: "hcp-users@humanconnectome.org"
Subject: Re: [HCP-Users] HCP_FIX
hcp_fix cleans both the volu
: Matt Glasser mailto:glass...@wustl.edu>>
Cc: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] HCP_FIX
hey matt,
the thing is, I didn't see anything in the hip_fix script the projec
-users-boun...@humanconnectome.org>>
on behalf of Shachar Gal mailto:gal.shac...@gmail.com>>
Date: Monday, November 19, 2018 at 3:30 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users
Dear experts,
I was was looking for some documentation regarding the differences between
the standard FSL FIX script, and the HCP's modified version, but could not
find such.
could you point me to such a documentation, if exists, or perhaps elaborate
briefly on the subject?
on the same subject, is
Dear Experts,
I have installed all required versions from packages kernlab, party, etc. in R
successfully, but after running hcp_fix I found the following error in
.fix.log. Please advice (see below):
/bin/bash: /Applications/workbench/bin_macosx64: is a directory
Error using read_gifti_file_st
He Leah,
It should not be necessary for you to change any of the lines you show
below from the FIX settings.sh file.
Of course, there are certainly lines after those lines in sections
labeled "Part I MATLAB settings", "Part II Octave settings", and "Part
III General Settings" that you will n
Dear experts,
I want to use the “hcp_fix" script for clean up of resting state data after HCP
pipelines. I am editing “settings.sh" and wanted to know if I have to edit
these lines copied below:
# Settings file for FIX
# Modify these settings based on your system setup
FIXVERSION=1.065
# (act
@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] hcp_fix and correlation maps
Exactly Matt, in principal what you explained below is what we need. The
wb_view only accepts spec or scene files (unless I am misunderstanding) and not
sure how to
mailto:glass...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: RE: [HCP-Users] hcp_fix and correlation maps
Thanks Matt.
Yes, fix.log showed the error location and after correcting it we now
: Osama Abdullah mailto:osama.abdul...@utah.edu>>
Date: Wednesday, April 5, 2017 at 5:54 PM
To: Matt Glasser mailto:glass...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: RE: [HCP-U
llah; hcp-users@humanconnectome.org
Subject: Re: [HCP-Users] hcp_fix and correlation maps
Unfortunately not all of the errors of ICA+FIX are reported to the main stderr.
You’ll need to look in the log files inside the directory created by ICA+FIX
to see what the error was (in matlab or R). There isn’t u
@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] hcp_fix and correlation maps
Dear HCP Experts,
We are applying the hcp_fix pipeline on Prisma-acquired data (according to the
Life Span protocol) and it completed without errors (although it took
significa
Dear HCP Experts,
We are applying the hcp_fix pipeline on Prisma-acquired data (according to the
Life Span protocol) and it completed without errors (although it took
significant effort on installing the proper R packages). Nonetheless, we cannot
find the resulting files that are labelled "clea
me.org<mailto:hcp-users@humanconnectome.org>"
mailto:HCP-Users@humanconnectome.org>>
Subject: [HCP-Users] hcp_fix bug
I am getting very similar errors to Nallin. Has this been resolved?
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Bioinformatics and Co
I am getting very similar errors to Nallin. Has this been resolved?
Timothy Hendrickson
Department of Psychiatry
University of Minnesota
Bioinformatics and Computational Biology M.S. Candidate
Office: 612-624-6441
Mobile: 507-259-3434 (texts okay)
___
an, Mr<mailto:michael.klein...@mail.mcgill.ca>;
hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] HCP_FIX Environment Setup
You’ll have to look into the logs to see if there has been some other error.
They are in several places… Also, do you ha
4, 2016 at 8:59 PM
To: Matt Glasser mailto:glass...@wustl.edu>>,
"hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: RE: [HCP-Users] HCP_FIX Environment Setup
Hi Matt,
Thanks again for the
ass...@wustl.edu>
Sent: Sunday, October 23, 2016 8:27 PM
To: Michael Kleinman, Mr<mailto:michael.klein...@mail.mcgill.ca>;
hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] HCP_FIX Environment Setup
Perhaps you need to delete the prior part
ectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: RE: [HCP-Users] HCP_FIX Environment Setup
Hi Matt,
Thanks for the fast response! I have now set up the configuration file
properly, but am now encountering the same issue seen in the th
...@wustl.edu>
Sent: Thursday, October 20, 2016 7:58 PM
To: Michael Kleinman, Mr<mailto:michael.klein...@mail.mcgill.ca>;
hcp-users@humanconnectome.org <mailto:hcp-users@humanconnectome.org>
Subject: Re: [HCP-Users] HCP_FIX Environment Setup
Perhaps you didn't set it to use compil
mailto:michael.klein...@mail.mcgill.ca>>
Date: Thursday, October 20, 2016 at 11:05 AM
To: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] HCP_FIX Environment Setup
Hello,
I am trying to app
Hello,
I am trying to apply the hcp_fix script to task data from the Human Connectome
Project, but am encountering difficulties when setting up the environment. I
have read through the README file; I setup the compiled Matlab version, and
pointed FSL_FIX_MCRROOT to the compiled Matlab version i
me.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] hcp_fix bug
Hi Matt,
"... " in last Email refer to
/home/fas/glahn/ny87/software/workbench/bin_linux64/
So before running fix_3_clean, I've set
WBC=&#x
l.com"
> Date: Wednesday, October 19, 2016 at 5:04 PM
>
> To: Matt Glasser
> Cc: "hcp-users@humanconnectome.org"
> Subject: Re: [HCP-Users] hcp_fix bug
>
> Hi Matt,
>
> I added all the paths needed in fix_3_clean, but still get the error. Is
> it possible
mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] hcp_fix bug
Hi Matt,
I added all the paths needed in fix_3_clean, but still get the error. Is it
possible because I add WBC as .../wb_command ?
Best,
Nailin
Sent from my iPh
e command.
>
> Peace,
>
> Matt.
>
> From: nailin yao
> Date: Wednesday, October 19, 2016 at 4:02 PM
> To: Matt Glasser
> Cc: "hcp-users@humanconnectome.org"
> Subject: Re: [HCP-Users] hcp_fix bug
>
> Hi Matt,
>
>
> I tried to run fi
me.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] hcp_fix bug
Hi Matt,
I tried to run fix_3_clean on matlab directly, and met the error message below:
fix_3_clean('.fix',0,1,2000)
TR =
0.7200
/bin/bash: -cifti-convert: command not found
Un
f you try running the
> fix_3_clean function with the parameters mentioned below?
>
> Peace,
>
> Matt.
>
> From: nailin yao
> Date: Monday, October 17, 2016 at 2:58 PM
> To: Matt Glasser
> Cc: "hcp-users@humanconnectome.org"
> Subject: Re: [HCP-Users] hcp_fix
: "hcp-users@humanconnectome.org<mailto:hcp-users@humanconnectome.org>"
mailto:hcp-users@humanconnectome.org>>
Subject: Re: [HCP-Users] hcp_fix bug
Hi Matt,
It's not compiled matlab.
Best,
Nailin
2016-10-17 13:53 GMT-04:00 Glasser, Matthew
mailto:glass...@wustl.edu>>:
Is
17, 2016 at 11:13 AM
> To: "hcp-users@humanconnectome.org"
> Subject: [HCP-Users] hcp_fix bug
>
> Hi ,
>
> I received the bug report when running hcp_fix for the last step:
>
> running FIX
>
> FIX Feature extraction for Melodic output directory:
> rfMRI_REST1_LR_nonlin_n
>"
mailto:hcp-users@humanconnectome.org>>
Subject: [HCP-Users] hcp_fix bug
Hi ,
I received the bug report when running hcp_fix for the last step:
running FIX
FIX Feature extraction for Melodic output directory:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica
create edge masks
run FAS
Hi ,
I received the bug report when running hcp_fix for the last step:
running FIX
FIX Feature extraction for Melodic output directory:
rfMRI_REST1_LR_nonlin_norm_hp2000.ica
create edge masks
run FAST
registration of standard space masks
extract features
FIX Classifying components in Me
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